Two-color microarray experiments: Technology and sources of variance

Methods of Information in Medicine

Volumn 44, Issue 3, 2005, Pages 400-404

  Repsilber, Dirk ^a,b   Ziegler, A ^a  

^a UNIVERSITY OF LÜBECK   (Germany)

^b UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

Author keywords

Agilent; Chip; Comparative hybridization; Gene expression; Microarray; Technical variance

Indexed keywords

COMPLEMENTARY DNA;

ALGORITHM; ANALYTICAL ERROR; ARTICLE; DNA HYBRIDIZATION; DNA MICROARRAY; HISTOGRAM; IMAGE ANALYSIS; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

EID: 22944471092     PISSN: 00261270     EISSN: None     Source Type: Journal    
DOI: 10.1055/s-0038-1633983     Document Type: Article

References (28)

1. Schena M. Microarray analysis. New Jersey: Wiley; 2003.
2. Tefferi A, et al. Primer on Medical Genomics, Part III: Microarray Experiments and Data Analysis. Mayo Clin Proc 2002; 77: 927-40.
3. Van Gelder RN, et al. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 1990; 87: 1663-7.
4. Klur S, et al. Evaluation of procedures of small-size samples for hybridization on microarrays. Genomics 2004; 83: 508-17.
5. Duggan DJ, et al. Expression profiling using cDNA microarrays. Nat Genet 1999; 21: 10-4.
6. Alwine J, Kemp D, Stark G. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 1977; 74 (12): 5350-4.
7. Southern E, et al. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 1992; 13 (4): 1008-17.
8. Lipshutz RJ, et al. High density synthetic oligonucleotide arrays. Nat Genet 1999; 21 (1, suppl): 20-4.
9. DeRisi J, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996; 14 (4): 457-60.
10. Eisen M, Brown P. DNA arrays for analysis of gene expression. Methods Enzymol 1999; 303: 179-205.
11. Katzer M, Kummert F, Sagerer G. Methods for automatic microarray image segmentation. IEEE Trans Nanobioscience 2003; 2 (4): 202-14.
12. King HC, Sinha AA. Gene Expression Profile Analysis by DNA Microarrays: Promise and Pitfalls. JAMA 2002; 286 (18): 2280-8.
13. Landgrebe J, et al. Efficient Two-Sample Designs for Microarray Experiments with Biological Replications. In Silico Biol 2004; 4: 0038.
14. Bretz F, et al. Design and Analysis of Two-color Microarray Experiments using Linear Models. Methods Inf Med 2005; 44: 423-30 (this issue).
15. http://www.agilent.com
16. Rishi AS, et al. DNA Microarrays: Gene Expression Profiling in Plants. In: Goyal A, Mehta SL, Lodha ML (eds). Reviews in Plant Biochemistry and Biotechnology 2002; 1: 81-100.
17. Parmigiani G, et al. The Analysis of Gene Expression Data, Heidelberg: Springer; 2003.
18. Sültmann H. cDNA microarrays for gene expression studies in complex disease. 2001; http://www.biometrie.uni-heidelberg.de/workshops/bamm2001/ talk_Sueltmann.pdf
19. Agilent Technologies. Agilent SurePrint Technology - Content centered microarray design enabling speed and flexibility. 2003; http://www. agilent.com.
20. Simon RM, et al. Design and Analysis of DNA Microarray Investigations. Heidelberg: Springer; 2003.
21. Repsilber D, Ziegler A. Sample selection for Microarray studies. Methods Inf Med 2005; 44: 461-7 (this issue).
22. Kane MD, et al. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 2000; 28 (22): 4552-7.
23. Ittrich C. Intensity-dependent Normalization for cDNA-Chips. Methods Inf Med 2005; 44: 418-22 (this issue).
24. Rahnenführer J. Image Analysis for cDNA Microarrays. Methods Inf Med 2005; 44: 405-7 (this issue).
25. Khomyakova EB, et al. Innovative instrumentation for microarray scanning and analysis: Application for characterization of oligonucleotide duplexes behaviour. Cell Mol Biol (Noisy-legrand) 2004; 50(3): 217-24.
26. Breit S, et al. Impact of pre-analytical handling on bone marrow mRNA gene expression. Br J Haematol 2004; 126: 231-43.
27. Watson SJ, et al. The "Chip" as a Specific Genetic Tool. Biol Psychiatry 2000; 48: 1147-56.
28. Brazma, A, et al. Minimum information about a microarray experiment (MIAME) - towards standards for microarray data. Nat Genet 2001; 29: 365-71.